Align D-lactate dehydrogenase (cytochrome) (EC 1.1.2.4) (characterized)
to candidate RR42_RS17300 RR42_RS17300 glycolate oxidase
Query= BRENDA::W1QLN6 (564 letters) >FitnessBrowser__Cup4G11:RR42_RS17300 Length = 497 Score = 201 bits (511), Expect = 6e-56 Identities = 130/426 (30%), Positives = 208/426 (48%), Gaps = 14/426 (3%) Query: 132 QRPVAVVYPENTEEVSAILKVCHKHKVPVVPFSGGTSLEGQFIPTRKGICIDLGKMNKIL 191 Q P+AV P+N ++V AIL++CH +VPVVP GTSL G +P G+ + L K +I+ Sbjct: 52 QVPMAVALPDNEDQVCAILRLCHSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIV 111 Query: 192 ELHKDDLDVVVQPAVGWEDLRDYLQDYNLMFGPDPGPG-AC-IGGMIGTSCSGTNAARYG 249 + VVQP V + + YNL + PDP AC IGG + + G + +YG Sbjct: 112 SVDVRSRTAVVQPGVRNLAISEAAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYG 171 Query: 250 TMKENVVGVTVVLADGTIVKTKKRPKKSSAGYNLTGLFIGSEGTLGIVTEATLKLHVKPR 309 NV+ V V +G +V+ + G +L IGSEG L +VTE ++KL KP+ Sbjct: 172 LTVHNVLRVRAVTMEGDVVEFGSE-APDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQ 230 Query: 310 YENVLVVAFPSLVDAANTVAEMVQRAIPANAIELLDENMMHYVNFSGETSSKYDELPTLM 369 V++ +F + N VA+++ I +E++D+ V D L+ Sbjct: 231 LAQVIMASFDDVAKGGNAVADVIGAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILL 290 Query: 370 LKLGGDSKESTQHVTRAVEQICKQHNRKSFRFAESDEEKFELWNARKVALWSTINYGKQT 429 + G +E + V R + ++ + + ++S+ E+ W+ RK A + G+ + Sbjct: 291 CESDGTPEEVAEEVER-MSEVLRASGASRIQVSQSEPERLRFWSGRKNAFPAA---GRIS 346 Query: 430 IDEDIQVWTTDVAVPISRLCQSLQETKDEISKAGLNASIVGHVGDGNYHAVILF---KKD 486 D + D +P + L+ ++ K GL V H GDGN H +ILF +D Sbjct: 347 PD----YYCMDGTIPRKHIGTLLKRIEEMERKYGLRCMNVFHAGDGNMHPLILFDGADQD 402 Query: 487 QYELTKKLVQGMIDRALLAEGTVTGEHGVGYGKRDYLIEEAGEDAVDLMRKIKMALDPNR 546 ++ + +++ + GTVTGEHGVG K + + + DL +K A DP R Sbjct: 403 EWHRAELFGSDILESCVELGGTVTGEHGVGVEKLNSMCVQFSAQERDLFFGVKAAFDPAR 462 Query: 547 ILNPDK 552 +LNPDK Sbjct: 463 LLNPDK 468 Lambda K H 0.316 0.135 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 622 Number of extensions: 31 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 564 Length of database: 497 Length adjustment: 35 Effective length of query: 529 Effective length of database: 462 Effective search space: 244398 Effective search space used: 244398 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory